Topic: metagenomics Goto Github

👇 Here are 643 public repositories matching this topic...

ayixon / rapdtool
metagenomics,Rapid Profiling and Deconvolution Tool for Metagenomes
User: ayixon
bioinformatics metagenomics metagenome-assembled-genomes microbial-taxonomy

benjjneb / dada2
metagenomics,Accurate sample inference from amplicon data with single nucleotide resolution
User: benjjneb
Home Page: http://benjjneb.github.io/dada2/
microbiome bioinformatics bioconductor taxonomy amplicon metagenomics metabarcoding

benjjneb / decontam
metagenomics,Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
User: benjjneb
Home Page: https://benjjneb.github.io/decontam/
microbiome bioinformatics contamination metagenomics amplicon metabarcoding

bigdatabiology / semibin
metagenomics,SemiBin: metagenomics binning with self-supervised deep learning
Organization: bigdatabiology
Home Page: https://semibin.rtfd.io/
assembly-binning bioinformatics deep-learning metagenomics self-supervised-learning

biobakery / maaslin2
metagenomics,MaAsLin2: Microbiome Multivariate Association with Linear Models
Organization: biobakery
Home Page: http://huttenhower.sph.harvard.edu/maaslin2
biobakery public tools bioconductor microbiome metagenomics differential-abundance-analysis false-discovery-rate repeated-measures multiple-covariates

biobakery / metaphlan
metagenomics,MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Organization: biobakery
Home Page: http://segatalab.cibio.unitn.it/tools/metaphlan/index.html
public tools biobakery python metagenomics

bioinformatics-centre / kaiju
metagenomics,Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
Organization: bioinformatics-centre
Home Page: http://kaiju.binf.ku.dk
metagenomics next-generation-sequencing bioinformatics taxonomic-classification taxonomy

bluenote-1577 / skani
metagenomics,Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.
User: bluenote-1577
average-nucleotide-identity bioinformatics metagenomics rust

bluenote-1577 / sylph
metagenomics,ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
User: bluenote-1577
average-nucleotide-identity k-mer metagenomics sketching-algorithm taxonomic-classification

cafferychen777 / ggpicrust2
metagenomics,Make Picrust2 Output Analysis and Visualization Easier
User: cafferychen777
Home Page: https://cafferychen777.github.io/ggpicrust2/
16s-rrna functional-data metagenomic-analysis metagenomics microbiome microbiota picrust2 tax4fun2 visualization

cami-challenge / camisim
metagenomics,CAMISIM: Simulating metagenomes and microbial communities
Organization: cami-challenge
Home Page: https://data.cami-challenge.org/participate
metagenomics simulation

dnbaker / dashing
metagenomics,Fast and accurate genomic distances using HyperLogLog
User: dnbaker
sketch-data-structures metagenomics indexing hyperloglog

ecogenomics / gtdbtk
metagenomics,GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Organization: ecogenomics
Home Page: https://ecogenomics.github.io/GTDBTk/
taxonomy species-assignments phylogenetics archaea bacteria nomenclature bioinformatics metagenomics

fbreitwieser / krakenuniq
metagenomics,🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
User: fbreitwieser
bioinformatics metagenomics

franciscozorrilla / metagem
metagenomics,:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
User: franciscozorrilla
Home Page: https://franciscozorrilla.github.io/metaGEM/
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis

galaxyproject / training-material
metagenomics,A collection of Galaxy-related training material
Organization: galaxyproject
Home Page: https://training.galaxyproject.org
usegalaxy training materials ngs tutorial metagenomics proteomics rnaseq chip-seq hacktoberfest

grimmlab / microbiomebestpracticereview
metagenomics,Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
Organization: grimmlab
Home Page: https://www.bit.cs.tum.de/
microbiome microbiome-analysis microbiome-workflow biomedical best-practices pipeline bioinformatics amplicon-sequencing assembly 16s-rrna

hadrieng / insilicoseq
metagenomics,:rocket: A sequencing simulator
User: hadrieng
Home Page: https://insilicoseq.readthedocs.io
bioinformatics illumina-sequencing sequencing simulation metagenomics

jtamames / squeezemeta
metagenomics,A complete pipeline for metagenomic analysis
User: jtamames
metagenomics pipeline metagenomes taxonomic-assignment

khyox / recentrifuge
metagenomics,Recentrifuge: robust comparative analysis and contamination removal for metagenomics
User: khyox
Home Page: http://www.recentrifuge.org
centrifuge clark comparative-genomics contamination kraken lmat low-biomass metagenomics nanopore ngs robustness

louiejtaylor / grabseqs
metagenomics,A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA
User: louiejtaylor
bioinformatics conda metagenomics ncbi-sra ngs python sra

merenlab / anvio
metagenomics,An analysis and visualization platform for 'omics data
Organization: merenlab
Home Page: http://merenlab.org/software/anvio
metagenomics metatranscriptomics pangenomics comparative-genomics science visualization bioinformatics phylogenomics population-genetics python

metagenome-atlas / atlas
metagenomics,ATLAS - Three commands to start analyzing your metagenome data
Organization: metagenome-atlas
Home Page: https://metagenome-atlas.github.io/
metagenomics annotation snakemake assembly genomic-binning functional-annotation taxonomic-classifications

metagentools / graphbin
metagenomics,✨🧬 Refined binning of metagenomic contigs using assembly graphs
Organization: metagentools
Home Page: https://graphbin.readthedocs.io/en/latest/
metagenomics binning contigs assembly-graph label-propagation

microbelab / deepmicrobes
metagenomics,DeepMicrobes: taxonomic classification for metagenomics with deep learning
User: microbelab
Home Page: https://doi.org/10.1093/nargab/lqaa009
deep-learning metagenomics next-generation-sequencing bioinformatics microbiome

microsud / tools-microbiome-analysis
metagenomics,A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
User: microsud
Home Page: https://microsud.github.io/Tools-Microbiome-Analysis/
microbiome-analysis microbial-communities microbiome-data amplicon-sequencing microbiota amplicon 16s-rrna metagenomics

mrolm / drep
metagenomics,Rapid comparison and dereplication of genomes
User: mrolm
bioinformatics metagenomics microbiology assembly microbial-genomes

nf-core / ampliseq
metagenomics,Amplicon sequencing analysis workflow using DADA2 and QIIME2
Organization: nf-core
Home Page: https://nf-co.re/ampliseq
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its

nf-core / eager
metagenomics,A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Organization: nf-core
Home Page: https://nf-co.re/eager
nextflow ancientdna adna pipeline pathogen-genomics population-genetics nf-core workflow metagenomics bioinformatics

nf-core / mag
metagenomics,Assembly and binning of metagenomes
Organization: nf-core
Home Page: https://nf-co.re/mag
workflow nextflow metagenomics assembly binning annotation nf-core pipeline bioinformatics nanopore

nf-core / taxprofiler
metagenomics,Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
Organization: nf-core
Home Page: https://nf-co.re/taxprofiler
metagenomics profiling taxonomic-profiling shotgun nf-core nextflow workflow pipeline classification microbiome

nf-core / viralrecon
metagenomics,Assembly and intrahost/low-frequency variant calling for viral samples
Organization: nf-core
Home Page: https://nf-co.re/viralrecon
viral metagenomics amplicon assembly variant-calling illumina pipeline workflow nextflow nf-core

ngless-toolkit / ngless
metagenomics,NGLess: NGS with less work
Organization: ngless-toolkit
Home Page: https://ngless.embl.de
haskell bioinformatics bioinformatics-pipeline samtools bwa next-generation-sequencing fastq-format fastq science ngs

pirovc / ganon
metagenomics,ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
User: pirovc
Home Page: https://pirovc.github.io/ganon/
metagenomics bioinformatics k-mer bloom-filter microbiome minimizers taxonomy genbank gtdb ncbi

ratschlab / metagraph
metagenomics,Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly
Organization: ratschlab
Home Page: http://metagraph.ethz.ch
graph dna alignment metagenomics search assembly

rhysnewell / aviary
metagenomics,A hybrid assembly and MAG recovery pipeline (and more!)
User: rhysnewell
assembly binning bioinformatics metagenomics workflow

ropensci / biomartr
metagenomics,Genomic Data Retrieval with R
Organization: ropensci
Home Page: https://docs.ropensci.org/biomartr
r genome-retrieval biomart database-retrieval ncbi-genbank genomics ensembl-servers sequenced-genomes proteome genome

seqan / lambda
metagenomics,LAMBDA – the Local Aligner for Massive Biological DatA
Organization: seqan
Home Page: https://github.com/seqan/lambda
bioinformatics blast blast-searches ncbi-taxonomy alignment metagenomics protein-sequences high-performance seqan

shenwei356 / kmcp
metagenomics,Accurate metagenomic profiling && Fast large-scale sequence/genome searching
User: shenwei356
Home Page: https://bioinf.shenwei.me/kmcp
kmer sketch searching metagenomics taxonomic-classification taxonomic-profiling scaled-minhash syncmers cobs sketching

soedinglab / metaeuk
metagenomics,MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics
Organization: soedinglab
metagenomics eukaryotes gene-prediction gene-discovery bioinformatics

soedinglab / mmseqs2
metagenomics,MMseqs2: ultra fast and sensitive search and clustering suite
Organization: soedinglab
Home Page: https://mmseqs.com
bioinformatics sequence-clustering profile-search sequence-search linclust mmseqs metagenomics alignment blast taxonomy

soedinglab / plass
metagenomics,sensitive and precise assembly of short sequencing reads
Organization: soedinglab
Home Page: https://plass.mmseqs.com
bioinformatics metagenomics sequence-assembler proteins opensource proteomics metatranscriptomics

spacegraphcats / spacegraphcats
metagenomics,Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Organization: spacegraphcats
Home Page: https://spacegraphcats.github.io/spacegraphcats/
bioinformatics k-mers metagenomics

steineggerlab / metabuli
metagenomics,Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.
Organization: steineggerlab
bioinformatics k-mer metagenomics taxonomic-classification taxonomy

sunbeam-labs / sunbeam
metagenomics,A robust, extensible metagenomics pipeline
Organization: sunbeam-labs
Home Page: http://sunbeam.readthedocs.io
metagenomics snakemake reproducible-research

torognes / vsearch
metagenomics,Versatile open-source tool for microbiome analysis
User: torognes
metabarcoding metagenomics chimera bioinformatics fastq fasta microbiome amplicon sequence-alignment clustering

verisimilitudex / dnanalyzer
metagenomics,Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools.
User: verisimilitudex
amino-acid-sequence bioinformatics dna-sequencing regulatory-elements transcriptomics protein-sequences genomics sequencing metagenomics dna

voutcn / megahit
metagenomics,Ultra-fast and memory-efficient (meta-)genome assembler
User: voutcn
Home Page: http://www.ncbi.nlm.nih.gov/pubmed/25609793
bioinformatics metagenomics succinct data-structures genomics genome-assembly

wrightonlabcsu / dram
metagenomics,Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
Organization: wrightonlabcsu
bioinformatics genomics metagenome-assembled-genomes metagenomics viral-genomics viral-metagenomics annotation microbiome

yiluheihei / microbiomemarker
metagenomics,R package for microbiome biomarker discovery
User: yiluheihei
Home Page: https://yiluheihei.github.io/microbiomeMarker
microbiome biomarker-discovery lefse metagenomics r differential-abundance-analysis r-package